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Title :   PHOSPHORIBOSYLDIPHOSPHATE SYNTHETASE IN COMPLEX WITH CADMIUM IONS

Authors :   T. A. Eriksen, A. Kadziola, S. Larsen

Date :   29 Mar 01 (Deposition) - 06 Feb 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (3x)

Keywords :   Open Alpha Beta Structure, Domain Duplication, Phosphoribosyltransferase Type I Fold, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. A. Eriksen, A. Kadziola, S. Larsen
Binding Of Cations In Bacillus Subtilis Phosphoribosyldiphosphate Synthetase And Their Role In Catalysis.
Protein Sci. V. 11 271 2002
PubMed-ID: 11790837 | Reference-DOI: 10.1110/PS.28502

Molecule 1 - RIBOSE-PHOSPHATE PYROPHOSPHOKINASE
	Chains	:	A, B
	EC Number	:	2.7.6.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PAB600
	Expression System Strain	:	HO773, IV
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PRS
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Synonym	:	PHOSPHORIBOSYLDIPHOSPHATE SYNTHETASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (3x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 10)

No.	Name	Count	Type	Full Name
1	ABM	2	Ligand/Ion	METHYL PHOSPHONIC ACID ADENOSINE ESTER
2	CD	4	Ligand/Ion	CADMIUM ION
3	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 18)

No.	Name	Count	Type	Full Name
1	ABM	6	Ligand/Ion	METHYL PHOSPHONIC ACID ADENOSINE ESTER
2	CD	-1	Ligand/Ion	CADMIUM ION
3	SO4	12	Ligand/Ion	SULFATE ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP B:227 , THR B:228 , ALA B:229 , GLY B:230 , THR B:231 , HOH B:1015 , HOH B:1029 , HOH B:1035	BINDING SITE FOR RESIDUE SO4 B 1001
02	AC2	SOFTWARE	ASP A:227 , THR A:228 , ALA A:229 , GLY A:230 , THR A:231	BINDING SITE FOR RESIDUE SO4 A 1002
03	AC3	SOFTWARE	ARG A:109 , SER B:52 , ARG B:54 , SER B:310 , VAL B:311 , SER B:312	BINDING SITE FOR RESIDUE SO4 B 1003
04	AC4	SOFTWARE	SER A:52 , ARG A:54 , SER A:310 , VAL A:311 , SER A:312 , HOH A:1016 , HOH A:1018 , ARG B:109	BINDING SITE FOR RESIDUE SO4 A 1004
05	AC5	SOFTWARE	HIS A:135 , ABM A:1009	BINDING SITE FOR RESIDUE CD A 1005
06	AC6	SOFTWARE	ASP A:174 , ASP A:223	BINDING SITE FOR RESIDUE CD A 1006
07	AC7	SOFTWARE	HIS B:135 , ABM B:1010	BINDING SITE FOR RESIDUE CD B 1007
08	AC8	SOFTWARE	ASP B:174 , ASP B:223 , HOH B:1033	BINDING SITE FOR RESIDUE CD B 1008
09	AC9	SOFTWARE	ARG A:101 , GLN A:102 , ARG A:104 , HIS A:135 , CD A:1005 , HOH A:1030 , PHE B:40 , ASP B:42 , GLU B:44	BINDING SITE FOR RESIDUE ABM A 1009
10	BC1	SOFTWARE	PHE A:40 , ASP A:42 , GLU A:44 , GLN A:46 , ARG B:101 , GLN B:102 , ARG B:104 , HIS B:135 , CD B:1007	BINDING SITE FOR RESIDUE ABM B 1010

(no "SS Bond" information available for 1IBS)

Asymmetric Unit

No.	Residues
1	Asp A:66	-	Pro A:67
2	Asp B:66	-	Pro B:67

(no "SAP(SNP)/Variant" information available for 1IBS)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PRPP_SYNTHASE	PS00114	Phosphoribosyl pyrophosphate synthase signature.	KPRS_BACSU	134-149	2	A:133-148 B:133-148

Biological Unit 1 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PRPP_SYNTHASE	PS00114	Phosphoribosyl pyrophosphate synthase signature.	KPRS_BACSU	134-149	6	A:133-148 B:133-148

(no "Exon" information available for 1IBS)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:297
 aligned with KPRS_BACSU | P14193 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:308
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308        
           KPRS_BACSU     9 NLKIFSLNSNPELAKEIADIVGVQLGKCSVTRFSDGEVQINIEESIRGCDCYIIQSTSDPVNEHIMELLIMVDALKRASAKTINIVIPYYGYARQDRKARSREPITAKLFANLLETAGATRVIALDLHAPQIQGFFDIPIDHLMGVPILGEYFEGKNLEDIVIVSPDHGGVTRARKLADRLKAPIAIIDKRRPRPNVAEVMNIVGNIEGKTAILIDDIIDTAGTITLAANALVENGAKEVYACCTHPVLSGPAVERINNSTIKELVVTNSIKLPEEKKIERFKQLSVGPLLAEAIIRVHEQQSVSYLF 316
               SCOP domains d1ibsa1 A:8-166 Phosphoribosylpyrophosphate synthetase                                                                                                         d1ibsa2 A:167-315 Phosphoribosyl         pyrophosphate synthetase                                                                                     SCOP domains
               CATH domains 1ibsA02 A:8-151,A:293-313  [code=3.40.50.2020, no name defined]                                                                                 1ibsA01 A:152-292  [code=3.40.50.2020, no name          defined]                                                                             1ibsA02              -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhh.....eeeee.....eeeee.......eeeee.....hhhhhhhhhhhhhhhhhhh...eeeeee...........--....hhhhhhhhhhhhhh..eeeee...hhhhhhhh...eeee.hhhhhhhhhhhhh...eeeee....hhhhhhhhhhhh...eeeee..---------.eee......eeeee..ee..hhhhhhhhhhhhhh...eeeee..ee....hhhhhhhhh...eeeee.............eeee.hhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------PRPP_SYNTHASE   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ibs A   8 NLKIFSLNSNPELAKEIADIVGVQLGKCSVTRFSDGEVQINIEESIRGCDCYIIQSTSDPVNEHIMELLIMVDALKRASAKTINIVIPYYGYARQDRK--SREPITAKLFANLLETAGATRVIALDLHAPQIQGFFDIPIDHLMGVPILGEYFEGKNLEDIVIVSPDHGGVTRARKLADRLKAPIAIIDKR---------MNIVGNIEGKTAILIDDIIDTAGTITLAANALVENGAKEVYACCTHPVLSGPAVERINNSTIKELVVTNSIKLPEEKKIERFKQLSVGPLLAEAIIRVHEQQSVSYLF 315
                                    17        27        37        47        57        67        77        87        97       | -|      117       127       137       147       157       167       177       187       197|        -|      217       227       237       247       257       267       277       287       297       307        
                                                                                                                           105  |                                                                                       198       208                                                                                                           
                                                                                                                              108

Chain B from PDB  Type:PROTEIN  Length:299
 aligned with KPRS_BACSU | P14193 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:310
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316
           KPRS_BACSU     7 DKNLKIFSLNSNPELAKEIADIVGVQLGKCSVTRFSDGEVQINIEESIRGCDCYIIQSTSDPVNEHIMELLIMVDALKRASAKTINIVIPYYGYARQDRKARSREPITAKLFANLLETAGATRVIALDLHAPQIQGFFDIPIDHLMGVPILGEYFEGKNLEDIVIVSPDHGGVTRARKLADRLKAPIAIIDKRRPRPNVAEVMNIVGNIEGKTAILIDDIIDTAGTITLAANALVENGAKEVYACCTHPVLSGPAVERINNSTIKELVVTNSIKLPEEKKIERFKQLSVGPLLAEAIIRVHEQQSVSYLF 316
               SCOP domains d1ibsb1 B:6-166 Phosphoribosylpyrophosphate synthetase                                                                                                           d1ibsb2 B:167-315 Phosphoribosyl         pyrophosphate synthetase                                                                                     SCOP domains
               CATH domains --1ibsB02 B:8-151,B:293-313  [code=3.40.50.2020, no name defined]                                                                                 1ibsB01 B:152-292  [code=3.40.50.2020, no name          defined]                                                                             1ibsB02              -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhh...........................eeeee.....hhhhhhhhhhhhhhhhhhh...eeeeee...........--....hhhhhhhhhhhhhh..eeeee...hhhhhhhh...eeee.hhhhhhhhhhh.....eeeee....hhhhhhhhhhhhh..eeeee..---------.eee......eeeee..ee..hhhhhhhhhhhhhh...eeeee..ee....hhhhhhhh....eeeee.............eeee.hhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------PRPP_SYNTHASE   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ibs B   6 DKNLKIFSLNSNPELAKEIADIVGVQLGKCSVTRFSDGEVQINIEESIRGCDCYIIQSTSDPVNEHIMELLIMVDALKRASAKTINIVIPYYGYARQDRK--SREPITAKLFANLLETAGATRVIALDLHAPQIQGFFDIPIDHLMGVPILGEYFEGKNLEDIVIVSPDHGGVTRARKLADRLKAPIAIIDKR---------MNIVGNIEGKTAILIDDIIDTAGTITLAANALVENGAKEVYACCTHPVLSGPAVERINNSTIKELVVTNSIKLPEEKKIERFKQLSVGPLLAEAIIRVHEQQSVSYLF 315
                                    15        25        35        45        55        65        75        85        95       105  |    115       125       135       145       155       165       175       185       195  |      -  |    215       225       235       245       255       265       275       285       295       305       315
                                                                                                                             105  |                                                                                       198       208                                                                                                           
                                                                                                                                108

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: PRTase-like (145)

Superfamily: PRTase-like (145)

Family: Phosphoribosylpyrophosphate synthetase-like (6)

Protein domain: Phosphoribosylpyrophosphate synthetase (5)

Bacillus subtilis [TaxId: 1423] (3)

1a	d1ibsa1	A:8-166
1b	d1ibsb1	B:6-166
1c	d1ibsb2	B:167-315
1d	d1ibsa2	A:167-315

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.2020, no name defined] (117)

Bacillus subtilis. Organism_taxid: 1423. (8)

1a	1ibsA02	A:8-151,A:293-313
1b	1ibsB02	B:8-151,B:293-313
1c	1ibsA01	A:152-292
1d	1ibsB01	B:152-292

(no "Pfam Domain" information available for 1IBS)

Asymmetric Unit(hide GO term definitions)

Chain A,B (KPRS_BACSU | P14193)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0004749	ribose phosphate diphosphokinase activity	Catalysis of the reaction: D-ribose 5-phosphate + ATP = 5-phospho-alpha-D-ribose 1-diphosphate + AMP + 2 H(+).
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0006015	5-phosphoribose 1-diphosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of 5-phosphoribose 1-diphosphate, also known as 5-phosphoribosyl-1-pyrophosphate.
	GO:0044249	cellular biosynthetic process	The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
	GO:0009165	nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:0009156	ribonucleoside monophosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of a ribonucleoside monophosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with phosphate on the sugar.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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	Cis Peptide Bonds
		Asp A:66 - Pro A:67	[ RasMol ]
		Asp B:66 - Pro B:67	[ RasMol ]

Biological Unit
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	KPRS_BACSU \| P14193	:	1dkr 1dku

1dkr	1DKR IS PRPP SYNTHETASE STRUCTURE CONTAINING SULFATE AT THE ACTIVE AND REGULATORY SITES
1dku	1DKU IS PRPP SYNTHETASE STRUCTURE CONTAINING NUCLEOTIDES AT THE ACTIVE AND REGULATORY SITES

Description

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Ligands, Modified Residues, Ions (3, 10)

Sites (10, 10)

SS Bonds (0, 0)

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